From 28083a1e39d581cad2ff2057828477efa771364a Mon Sep 17 00:00:00 2001
From: jarathomas <jaratthomas@gmail.com>
Date: Wed, 8 May 2024 13:29:53 -0400
Subject: [PATCH] bug squash: fixed indiv probabilities

---
 src/insilicova/_sampler/sampler.cpp | 10 +++++-----
 src/insilicova/api.py               |  4 ++--
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/insilicova/_sampler/sampler.cpp b/src/insilicova/_sampler/sampler.cpp
index b90269e..c9b6487 100644
--- a/src/insilicova/_sampler/sampler.cpp
+++ b/src/insilicova/_sampler/sampler.cpp
@@ -396,11 +396,11 @@ void Sampler::count_current(double *ptr_indic,
         }
     }
 
-    // loop over all inidviduals
+    // loop over all individuals
     for (int n = 0; n < N; ++n) {
         // cause of this death
         int c_current = (int) y_new(n);
-        // add to toal counts
+        // add to total counts
         ptr_count_c[c_current] += 1;
         // loop over all symptoms
         for (int s = 0; s < S; ++s) {
@@ -515,7 +515,7 @@ void Sampler::trunc_beta2(py::array_t<double> prior_a, double prior_b,
                     }
                     upper = std::min(upper, trunc_max);
                 }
-                // if range is invalide, use higher case
+                // if range is invalid, use higher case
                 if (lower >= upper) {
                     proxy_new_pbase(s, c.cast<int>()) = upper;
                 } else {
@@ -617,7 +617,7 @@ void Sampler::trunc_beta(py::array_t<double> prior_a, double prior_b,
                     }
                     upper = std::min(upper, trunc_max);
                 }
-                // if range is invalide, use higher case
+                // if range is invalid, use higher case
                 if (lower >= upper) {
                     proxy_new_pbase(s.cast<int>(), c) = upper;
                 } else {
@@ -893,7 +893,7 @@ void Sampler::fit(py::array_t<double> prior_a, double prior_b,
         }       
     }
 
-    // reinitiate after checking impossible
+    // re-initiate after checking impossible
     if (!is_added) {
         for (int sub = 0; sub < N_sub; ++sub) {
             int fix = 0;
diff --git a/src/insilicova/api.py b/src/insilicova/api.py
index 013667d..92f0d83 100644
--- a/src/insilicova/api.py
+++ b/src/insilicova/api.py
@@ -1327,7 +1327,6 @@ def _sample_posterior(self):
         N_thin = int((N_gibbs - burn) / (thin))
         probbase_gibbs = np.zeros((N_thin, S, C))
         levels_gibbs = np.zeros((N_thin, N_level))
-        pnb_mean = np.zeros((N, C))
         p_gibbs = np.zeros((N_thin, N_sub, C))
         pnb_mean = np.zeros((N, C))
         naccept = [0] * N_sub
@@ -1396,10 +1395,11 @@ def _sample_posterior(self):
                 # self.burnin = self.n_sim / 2
                 N_gibbs = int(np.trunc(N_gibbs * (2 ** (add - 1))))
                 burn = 0
-                N_thin = int((N_gibbs - burn) / (thin))
+                N_thin = int((N_gibbs - burn) / thin)
                 probbase_gibbs = np.zeros((N_thin, S, C))
                 levels_gibbs = np.zeros((N_thin, N_level))
                 p_gibbs = np.zeros((N_thin, N_sub, C))
+                pnb_mean = np.zeros((N, C))
                 warnings.warn(
                     f"Not all causes with CSMF > {self.conv_csmf} are "
                     f"convergent.\n Increase chain length with another "